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Yes, the process is Multi-Threaded: In the tools|Configuration|Simultaneous connections menu you can configure the number of threads. Note that Win9x has an internal limit of 64 threads, and the unregistered version will only let you use up to 3 connections.
Since it's multi-threaded, there are no reasons to use 2 copies of it, since they will be wasting the same resources (windows connections).
